Molecular Biotechnology最新文献

{"title":"Computational Modelling and Molecular Docking of Industrial Leather Enzymes.","authors":"Nikita Sharma, Suneetha Vuppu","doi":"10.1007/s12033-023-00689-z","DOIUrl":"10.1007/s12033-023-00689-z","url":null,"abstract":"<p><p>Leather is one of the widely traded commodities globally. It is a strategically important sector for the economic and industrial development of the country. However, the leather industry is perceived as a highly polluting industry. It produces huge amounts of solid and liquid wastes, and if these wastes are not properly treated and disposed of, then it tends to deteriorate the quality of soil and water, as well as cause emanations of smell and noxious gases into the surrounding. The current paper provides information about industrial leather enzymes, primarily collagenase, tannase, and lecithinase. In this study, enzymes such as collagenase, tannase, and lecithinase had a pivotal role in leather industries and their action in the bioremediation of leather effluents was further analysed and docked with a diverse range of compounds (ligands), with an optimal binding affinity score was determined. All interactions between protein ligands were depicted, which will help us with future research. Furthermore, this method can be tested practically, and other parameters can be studied in the future. Further, applications of enzymes and their hydrolyse by-products have also been highlighted in a variety of industries, including the pharmaceutical, cosmetic, agricultural, medical, and food sectors. Subsequently, this finding provides an innovative and broader goal for various sectors in terms of sustainability, stabilisation, and identifying research gaps that can guide modern industries and research scientists.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2847-2865"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10809555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conquering Limitations: Exploring the Factors that Drive Successful Agrobacterium-Mediated Genetic Transformation of Recalcitrant Plant Species.","authors":"Nafiseh Aboofazeli, Solmaz Khosravi, Hedayat Bagheri, Stephen F Chandler, Shen Q Pan, Pejman Azadi","doi":"10.1007/s12033-024-01247-x","DOIUrl":"10.1007/s12033-024-01247-x","url":null,"abstract":"<p><p>Agrobacterium-mediated transformation is a preferred method for genetic engineering and genome editing of plants due to its numerous advantages, although not all species exhibit transformability. Genetic engineering and plant genome editing methods are technically challenging in recalcitrant crop plants. Factors affecting the poor rate of transformation in such species include host genotype, Agrobacterium genotype, type of explant, physiological condition of the explant, vector, selectable marker, inoculation method, chemical additives, antioxidative compounds, transformation-enhancing compounds, medium formulation, optimization of culture conditions, and pre-treatments. This review provides novel insights into the key factors involved in gene transfer facilitated by Agrobacterium and proposes potential solutions to overcome existing barriers to transformation in recalcitrant species, thereby contributing to improvement programs for these species. This review introduces the key factors that impact the effectiveness of a molecular breeding program using Agrobacterium-mediated transformation, specifically focusing on recalcitrant plant species.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3010-3026"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Culture Optimization to Produce High Yields of Mycosporine-Like Amino Acids by Fischerella sp. F5.","authors":"Shayan Salehian, Melika Saadatbakht, Maryam Tabarzad, Tahereh Hosseinabadi","doi":"10.1007/s12033-023-00854-4","DOIUrl":"10.1007/s12033-023-00854-4","url":null,"abstract":"<p><p>Fischerella sp. is a valuable source of active metabolites, including UV-protecting compounds, among which mycosporin-like amino acids (MAAs) can be mentioned. Mycosporine-like amino acids are attractive secondary metabolites of a wide range of microorganisms, including microalgae and cyanobacteria. Enhanced production of MAAs has been studied in different sources. This study aimed to optimize the phosphate and nitrate concentrations of the culture medium on BG11 to maximize MAAs production from Fischerella sp. F5, using response surface methodology. The extraction process from the cultures, grown in adjusted conditions, was also optimized. The results confirmed that increasing both, nitrate and phosphate concentration, in the culture medium had a positive effect on the MAAs production by Fischerella sp. F5. While, optimization of the extraction process was not led to a highly accurate predictive model; temperature, sonication time, methanol ratio, and solvent/biomass ratio exhibited significant effects on the final MAAs' concentration in partially purified extracts. In general, more optimization cultures studies need to complete these findings in reference to MAAs production and extraction from Fischerella sp. F5, for commercial-scale applications.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3109-3119"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10084267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Production Enhancement of Bacterial Cellulase Cocktail Using Potato Peels Waste Feedstock and Combination of Water Hyacinth Root and Pea Pod Extract as Natural Nutrient Media: Application in Bioconversion of Potato Peels.","authors":"Neha Srivastava, Pathan Ahemad Khan, Basant Lal, Rajeev Singh, Asad Syed, Abdallah M Elgorban, Meenakshi Verma, P K Mishra, Anthonia O'Donovan","doi":"10.1007/s12033-023-00789-w","DOIUrl":"10.1007/s12033-023-00789-w","url":null,"abstract":"<p><p>Solid wastes are the major contributors in global environmental pollution and their management is the need of urgency towards development of sustainable world. In the present work, solid waste of potato peels has been used as feedstock for fermentation of bacterial cellulase production and substrate for enzymatic hydrolysis via this enzymes cocktail. Additionally, liquid extracts of pea pod and root of water hyacinth wastes have been used to complete nutritional requirements and moisture balance in SSF process during the course of enzyme production. At optimum feedstock concentration of 6.0 g PPW and 10:40 extract-based moisture ratio of WHR and Ppw, Bacillus sp. produced 15 U/gds FP in 18 h, whereas maximum 36 U/gds BGL and 42 U/gds EG have been recorded in 24 h of SSF. Temperature 35 °C and pH 5.5 were optimum for enzyme production while the produced enzyme was thermally stable upto 30 h at 35 °C with 100% pH stability upto 14 h and 77% relative activity at 34 h. The optimized bacterial enzymes have been used for bioconversion of PPW biomass and 26 g/L glucose has been recorded at a hydrolytic temperature of 50 °C and pH 5.0. The study may have feasible promising scope in cellulosic biorefineries and waste management.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3089-3096"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9775981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring Microbial Contributions to Nutraceutical Production: From Natural to Designed Foods.","authors":"Babita Thakur, Sukhminderjit Kaur, Nitu Rani, Rajinder Kaur, Sudhir Kumar Upadhyay, Manikant Tripathi","doi":"10.1007/s12033-023-00937-2","DOIUrl":"10.1007/s12033-023-00937-2","url":null,"abstract":"<p><p>For ages, societies throughout the world have used fermentation as a traditional method for food processing and preservation, helping to create a wide range of staple foods and delicacies. Due to its possible health advantages, mostly attributable to the inclusion of bioactive substances known as nutraceuticals, fermented foods have attracted a lot of interest recently. This in-depth analysis examines the wide range of nutraceuticals present in fermented foods, as well as how they are made, what health benefits they may have, and how they may be used in the nutraceutical and functional food businesses. By stressing how important fermented foods are as a source of beneficial bioactive components that support human health and well-being. Numerous bioactive substances found in fermented foods have been the subject of recent scientific studies. These molecules may find use in the pharmaceutical and nutraceutical sectors. Streptococcus thermophilus, Lactobacillus gasseri, Lactobacillus delbrueckii, Lactobacillus bulgaricus, and Lactobacillus johnsonii are just a few examples of the probiotic bacteria that live in fermented foods and formulas. This review elucidates the importance of microorganisms sourced from fermented foods as potent agents for diverse nutraceuticals and their potential role in preventing various diseases whilst serving as functional food supplements.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2946-2961"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72014657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of HSP90 in Type 2 Diabetes Mellitus and Its Association with Liver Diseases.","authors":"V Nithyasree, P Magdalene, P K Praveen Kumar, J Preethi, M Michael Gromiha","doi":"10.1007/s12033-024-01251-1","DOIUrl":"10.1007/s12033-024-01251-1","url":null,"abstract":"<p><p>Non-alcoholic fatty acid liver disease (NAFLD), non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) are the fatal liver diseases which encompass a spectrum of disease severity associated with increased risk of type 2 diabetes mellitus (T2DM), a metabolic disorder. Heat shock proteins serve as markers in early prognosis and diagnosis of early stages of liver diseases associated with metabolic disorder. This review aims to comprehensively investigate the significance of HSP90 isoforms in T2DM and liver diseases. Additionally, we explore the collective knowledge on plant-based drug compounds that regulate HSP90 isoform targets, highlighting their potential in treating T2DM-associated liver diseases. Furthermore, this review focuses on the computational systems' biology and next-generation sequencing technology approaches that are used to unravel the potential medicine for the treatment of pleiotropy of these 2 diseases and to further elucidate the mechanism.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2997-3009"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Analysis of Calotropis procera-Derived Phytochemicals Targeting 3CL Proteoase of SARS-CoV-2.","authors":"Tayyaba Shafique, Mohsin Javed, Muhammad Ali, Shahid Iqbal, Muhammad Faizan, Ammar Zidan, Ali Bahadur, Sajid Mahmood, Fadi Jaber, Khalid M Alotaibi, Matar Alshalwi","doi":"10.1007/s12033-024-01253-z","DOIUrl":"10.1007/s12033-024-01253-z","url":null,"abstract":"<p><p>The coronavirus known as SARS-CoV-2 has enveloped virions with single-stranded positive-sense RNA genome. It infects mammals, including humans, via the respiratory tract. The non-structural protein of coronavirus, main protease (3CLp) is a key enzyme in the disease's progression. This study aimed to screen phytochemicals derived from Calotropis Procera as potential drugs against 3CLp. Through database search, 50 phytochemicals were identified in the Calotropis sp. To evaluate the possible drug-like properties of these phytochemicals, the studies like, ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) analysis, molecular docking and density functional theory (DFT) were performed. Furthermore, GC-MS was performed using water and ethanolic extracts from the plant leaves. The ADMET analysis and docking results showed 11 phytochemicals as probable drug candidates against 3CLp of SARS-CoV-2. All these phytochemicals showed ≥ - 4.3 kcal/mol binding affinity, similar to previously reported inhibitors. Furthermore, based on band energy gap, EHOMO, ELUMO, and DFT analyses, it was shown that these phytochemicals had a significant level of reactivity necessary for the interaction. Among all, the phytochemicals uscharin, voruscharin, frugoside, coroglaucigenin, and benzoylisolineolone may be considered the top 5 drug-like candidates against 3CLp. Furthermore, the selected phytochemicals may be employed for in vitro and in vivo studies for the advancement of a probable drug alongside SARS-CoV-2.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3296-3309"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring Natural Compounds as Potential CDK4 Inhibitors for Therapeutic Intervention in Neurodegenerative Diseases through Computational Analysis.","authors":"Neetu Rani, Pravir Kumar","doi":"10.1007/s12033-024-01258-8","DOIUrl":"10.1007/s12033-024-01258-8","url":null,"abstract":"<p><p>CDK4 is a member of the serine-threonine kinase family, which has been found to be overexpressed in a plethora of studies related to neurodegenerative diseases. CDK4 is one of the most validated therapeutic targets for neurodegenerative diseases. Hence, the discovery of potent inhibitors of CDK4 is a promising candidate in the drug discovery field. Firstly, the reference drug Palbociclib was identified from the available literature as a potential candidate against target CDK4. In the present study, the Collection of Open Natural Products (COCONUT) database was accessed for determining potential CDK4 inhibitors using computational approaches based on the Tanimoto algorithm for similarity with the target drug, i.e., Palbociclib. The potential candidates were analyzed using SWISSADME, and the best candidates were filtered based on Lipinski's Rule of 5, Brenk, blood-brain barrier permeability, and Pains parameter. Further, the molecular docking protocol was accessed for the filtered compounds to anticipate the CDK4-ligand binding score, which was validated by the fastDRH web-based server. Based on the best docking score so obtained, the best four natural compounds were chosen for further molecular dynamic simulation to assess their stability with CDK4. In this study, two natural products, with COCONUT Database compound ID-CNP0396493 and CNP0070947, have been identified as the most suitable candidates for neuroprotection.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3310-3329"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent Review on the Extraction and Qualitative Assay of Cysteine and Other Amino Acids from Vellore Feather Waste and Molecular Docking Studies of Cysteine for Pharmacological Applications.","authors":"Sathvika Kamaraj, Suneetha Vuppu","doi":"10.1007/s12033-023-00862-4","DOIUrl":"10.1007/s12033-023-00862-4","url":null,"abstract":"<p><p>Products produced from waste are a relatively recent innovation. Feather substrates are abundant in keratin content and improper disposal can cause ecosystem contamination. However, these pollutants can be transformed into value-added products for industrial application. Physical, chemical and cutting-edge microbiological methods were utilized for decomposing keratin and aid in the identification and estimation of amino acids from poultry feather wastes. These beneficial approaches are receiving more attention due to their retrieval of harmless and value added byproducts. These keratin-based compounds are used widely in pharmaceutical, livestock feed, fertilizer, and a variety of other industrial sectors. Since keratin is primarily consisting of amino acids, it can be utilized to affirm and estimate the amino acids in these feather substrates. This study primarily highlights the various methodologies employed for the qualitative estimation of amino acids in feather waste samples and the inhibitory activity of keratinase enzyme by EDTA and pepstatin in order to accumulate amino acids for drug delivery purpose and their importance in various pharmaceutical industries. In addition to that, molecular docking studies of cysteine with many standard pharmaceutical drugs like acetaminophen, pethidine, methylphenidate, carbamazepine, cillin and amlodipine were performed using autodock to demonstrate how cysteine greatly reduces conventional drug toxicity and its side effects.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2902-2930"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10321855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study of the Immune Infiltration and Sonic Hedgehog Expression Mechanism in Synovial Tissue of Rheumatoid Arthritis-Related Interstitial Lung Disease under Machine Learning CIBERSORT Algorithm.","authors":"Qunqun Lu, Yizhen Jiang, Xiaofeng Cang, Jiaojiao Pan, Xiaowen Shen, Ruoyu Tang, Zhe Zhou, Yiwen Zhu","doi":"10.1007/s12033-024-01245-z","DOIUrl":"10.1007/s12033-024-01245-z","url":null,"abstract":"<p><p>Rheumatoid arthritis-related interstitial lung disease (RA-ILD) is one of the common complications in patients with RA, which affects their quality of life. The CIBERSORT algorithm is widely employed to determine the proportion of immune cells (ICs) in diseased tissues, while the Sonic Hedgehog (Shh) signaling pathway, as an imperative regulatory factor, has also attracted attention in the pathology of RA-ILD. This work was to explore the mechanisms of RA-ILD immune infiltration and synovial tissue (ST) Shh expression based on the CIBERSORT algorithm. The differential genes of RA-ILD were subjected to pathway enrichment analysis using R language. The content and proportion of 22 types of ICs in RA-ILD lung tissues were analyzed using machine learning-based CIBERSORT algorithm. Meanwhile, immunoblotting was employed to detect and analyze the expression of Shh, Smoothened (Smo), and bone morphogenetic proteins (BMPs) proteins in ST samples from RA-ILD and Ctrl groups (RA patients without ILD). The hub target genes in the protein network associated with RA-ILD include BSG, CCL2, CTLA4, FGFBP1, GLI1, HHIP, HLA-DRB1, IFNAR1, IL17A, IL23A, IL-6, INPP4A, LILRB1, MUC5B, PADI4, PPM1A, PTCH1, PTPN22, RSPO4, Shh, SMO, STAT4, SUFU, TAOK2, TIMP2, and TWSG1, which are involved in multiple pathways, such as B cell regulation, transcription factors of the Shh pathway, and ST immune tolerance-related pathways. In the immunological analysis of RA-ILD using the CIBERSORT algorithm, HLA (r = - 0.26), PTPN22 (r = - 0.36), STAT4 (r = - 0.18), IL-6 (r = - 0.17), CTLA4 (r = - 0.27), and PADI4 (r = - 0.21) were all found to exhibit negative correlations with CD4+T cells (P < 0.05). Monocytes were found to be more abundant in RA-ILD patients' serum versus the Ctrl group. Shh, Smo, and BMP expressions were drastically lower in the RA-ILD group versus Ctrl group (P < 0.05). Significant immune cell infiltration was observed in the lung tissues of RA-ILD patients. Further analysis utilizing the CIBERSORT algorithm revealed alterations in the proportions of different IC subtypes, indicating their association with disease severity and prognosis. Moreover, there was a significant decrease in the expression levels of Shh, Smo, and BMP. These findings underscore the importance of immune cells in the pathophysiology of RA-ILD and suggest a potential involvement of the Shh signaling pathway in the pathogenesis of RA-ILD.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3217-3233"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}